Religion is also harmful (and again, this is just my own opinion) because it discourages critical thought, replacing it with faith.

I'm actually not sure to what degree this is true for religion in general. The emphasis on faith-in-itself seems to be mainly a Christian thing to me, although it's contaminated a lot of later (i.e. New Age) thought in the Christian cultural sphere; what I've read of Islam, for example, puts a pretty heavy emphasis on scholarship, and doesn't seem to isolate religious observations from empirical confirmation nearly to the same degree that Christianity does. The same goes for Buddhism, for several branches of occultism, and even for some minor Christian traditions, especially prior to the Enlightenment.

I think a fully general objection to religious thought would have to be a bit more subtle: even when a religion contains a tradition of inquiry, even when clerical roles look a lot like research positions, usually only confirming evidence is accepted. This doesn't have quite the same structure as faith in the modern Christian sense: tautological belief isn't thought of as virtuous. But the bottom line is already written, and arguments are only respected insofar as they provide support for it. Critical thought isn't discouraged, but it's only thought of as beneficial insofar as it serves preexisting goals. (Eliezer gets into this a bit in "Avoiding Your Belief's Real Weak Points", although I don't think it's limited to orthodox Judaism by any means.) Actually, I don't even think this is specific to religion: lots of identity groups behave in similar ways.